rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE11620.yaml

@@ -0,0 +1,33 @@
+--- 
+:description: We have enginereed S. cerevisiae to produce high titers of Artemisinic acid, an anti-malarial drug precursor. Here we compare the gene expression profiles of the producer strain (EPY330) and a strain in which the last enzyme of the pathway (CYP71AV1, AMO) was inactivated by a point mutation (EPY338).
+:arrays: 
+  GSM294795: 
+    condition: EPY338/EPY330_72h
+  GSM294796: 
+    condition: EPY338/EPY330_72h
+  GSM294797: 
+    condition: EPY338/EPY330_72h
+  GSM294786: 
+    condition: EPY338/EPY330_24h
+  GSM294798: 
+    condition: EPY338/EPY330_72h
+  GSM294787: 
+    condition: EPY338/EPY330_24h
+  GSM294799: 
+    condition: EPY338/EPY330_72h
+  GSM294788: 
+    condition: EPY338/EPY330_24h
+  GSM294789: 
+    condition: EPY338/EPY330_24h
+  GSM294790: 
+    condition: EPY338/EPY330_48h
+  GSM294791: 
+    condition: EPY338/EPY330_48h
+  GSM294792: 
+    condition: EPY338/EPY330_48h
+  GSM294793: 
+    condition: EPY338/EPY330_48h
+  GSM294794: 
+    condition: EPY338/EPY330_48h
+:title: Artemisinic Acid Production Stress in Yeast
+:platform: GPL6907

data/install_scripts/GEO/series/GSE11621.yaml

@@ -0,0 +1,31 @@
+--- 
+:description: |-
+  Comparison of WT, xrn1 delta and upf1 delta strains were used in a tiling array to yield genomic regions regulated by these proteins
+  The supplementary CHP files record either the signal in log2 space or the p-values in linear space, per TAS output.  The CHP files are further divided between UPF1 delta vs. WT and XRN1 delta vs. WT.
+:arrays: 
+  GSM294850: 
+    condition: dUPF1
+  GSM294851: 
+    condition: dXRN1
+  GSM294852: 
+    condition: dXRN1
+  GSM294853: 
+    condition: dXRN1
+  GSM294854: 
+    condition: dXRN1
+  GSM294843: 
+    condition: wt
+  GSM294844: 
+    condition: wt
+  GSM294845: 
+    condition: wt
+  GSM294846: 
+    condition: wt
+  GSM294847: 
+    condition: dUPF1
+  GSM294848: 
+    condition: dUPF1
+  GSM294849: 
+    condition: dUPF1
+:title: Identification of genomic regions regulated by the Xrn1 and Upf1 proteins
+:platform: GPL7250

data/install_scripts/GEO/series/GSE11651.yaml

@@ -0,0 +1,94 @@
+--- 
+:description: |-
+  Our study involves a transcriptomic approach to the analysis of industrial yeast metabolism. Historically, among the hundreds of yeast species, Saccharomyces cerevisiae has played an important role in scientific investigations and industrial applications, and it is universally acknowledged as one of the model systems for eukaryotic organisms. Yeast is also an important component of the wine fermentation process and determines various attributes of the final product.
+  Our research takes a holistic approach to the improvement of industrial yeast strains by integrating large data sets from various yeast strains during fermentation. This means that analysis can be done in such a way as to co-evaluate several parameters simultaneously to identify points of interest and target genes for metabolic engineering.
+  Eventually we hope to construct an accurate information matrix and a more complete cellular map for the fermenting yeast. This will enable accurate model-building for industrial yeast and facilitated the design of intelligent yeast improvement strategies which can be applied via traditional avenues of molecular biology.
+:arrays: 
+  GSM296856: 
+    condition: Day5 BM45
+  GSM291002: 
+    condition: Day14 VIN13
+  GSM290993: 
+    condition: Day14 BM45
+  GSM296857: 
+    condition: Day5 BM45
+  GSM291003: 
+    condition: Day14 VIN13
+  GSM290994: 
+    condition: ay14 DV10
+  GSM296858: 
+    condition: Day5 EC1118
+  GSM291554: 
+    condition: Day5 EC1118
+  GSM290995: 
+    condition: ay14 DV10
+  GSM296859: 
+    condition: Day5 EC1118
+  GSM291555: 
+    condition: Day5 BM45
+  GSM291445: 
+    condition: Day2 EC1118
+  GSM291115: 
+    condition: Day2 285
+  GSM290996: 
+    condition: ay14 DV10
+  GSM296860: 
+    condition: Day5 VIN13
+  GSM291523: 
+    condition: Day2 BM45
+  GSM291435: 
+    condition: Day2 EC1118
+  GSM291116: 
+    condition: Day2 285
+  GSM290997: 
+    condition: Day14 EC1118
+  GSM296861: 
+    condition: Day5 VIN13
+  GSM291524: 
+    condition: Day2 BM45
+  GSM291117: 
+    condition: Day2 285
+  GSM290998: 
+    condition: Day14 EC1118
+  GSM291525: 
+    condition: Day5 VIN13
+  GSM291140: 
+    condition: Day5 285
+  GSM290999: 
+    condition: Day14 EC1118
+  GSM291141: 
+    condition: Day5 285
+  GSM290989: 
+    condition: Day2 DV1
+  GSM290901: 
+    condition: Day2 VIN13
+  GSM291538: 
+    condition: Day5 DV10
+  GSM291439: 
+    condition: Day2 EC1118
+  GSM291142: 
+    condition: Day5 285
+  GSM290990: 
+    condition: Day2 DV1
+  GSM290902: 
+    condition: Day2 VIN13
+  GSM292045: 
+    condition: Day14 VIN13
+  GSM291539: 
+    condition: Day5 DV10
+  GSM291462: 
+    condition: Day2 BM45
+  GSM291000: 
+    condition: Day14 285
+  GSM290991: 
+    condition: Day2 DV1
+  GSM290903: 
+    condition: Day2 VIN13
+  GSM291540: 
+    condition: Day5 DV10
+  GSM291001: 
+    condition: Day14 285
+  GSM290992: 
+    condition: Day14 BM45
+:title: Transcriptomic profiling of five industrial wine yeast strains at three time points during allcoholic fermentation
+:platform: GPL2529

data/install_scripts/GEO/series/GSE11754.yaml

@@ -0,0 +1,29 @@
+--- 
+:description: Metabolite concentrations can regulate gene expression, which can in turn regulate metabolic activity. The extent to which functionally related transcripts and metabolites show similar patterns of concentration changes, however, remains unestablished.  We have therefore measured and analyzed the metabolomic (previously published in Brauer et al., PMID 17159141) and transcriptional responses (presented here) of Saccharomyces cerevisiae to carbon and nitrogen starvation.
+:arrays: 
+  GSM290982: 
+    condition: C-8
+  GSM290983: 
+    condition: N-0.16
+  GSM290984: 
+    condition: N-0.5
+  GSM290985: 
+    condition: N-1
+  GSM290986: 
+    condition: N-2
+  GSM290987: 
+    condition: N-4
+  GSM290988: 
+    condition: N-8
+  GSM290977: 
+    condition: C-0.16
+  GSM290978: 
+    condition: C-0.5
+  GSM290979: 
+    condition: C-1
+  GSM290980: 
+    condition: C-2
+  GSM290981: 
+    condition: C-4
+:title: Transcriptional responses of Saccharomyces cerevisiae to carbon and nitrogen deprivation
+:platform: GPL2883

data/install_scripts/GEO/series/GSE11799.yaml

@@ -0,0 +1,59 @@
+--- 
+:description: |-
+  Background
+  We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we demonstrated the transferability of this respiratory phenotype in the presence of up to 100 g/L glucose to a yeast strain in which only HXT1-7 had been deleted. In this study, we wanted to examine the basis of the respiratory phenotype of the resultant strain, V5.TM6*P, by comparing its transcriptome with that of its parent, V5, at different glucose concentrations.
+  Results
+  cDNA array analyses revealed that alterations in gene expression that occur when transitioning from a respiro-fermentative (V5) to a respiratory (V5.TM6*P) strain, are very similar to those in cells undergoing a diauxic shift. Highly complete collections of known genes of the TCA cycle, glyoxylate cycle and respiratory chain were identified, consistent with a respiratory metabolism. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4, Cat8 and Mig1, and using this in combination with verified binding consensus sequences, to identify genes likely to be regulated by one or more of these transcription factors. Of the induced genes of our dataset, 77 % had binding sites for Hap2/3/5 (Hap4 is an activator of this complex), with 72 % having at least two (the latter set being more induced than the former). This is relevant since Hap4 is known to be involved in the transcriptional activation of respiratory genes and other mitochondrial functions. In addition, 13 % of genes were found to have a binding site for Cat8, which together with its complexes with Sip4 have previously been identified as mediating de-repression of a number of genes during the diauxic shift. Finally, 21 % of genes had a binding site for Mig1 which is a transcriptional repressor involved in glucose repression. Unexpectedly, both the up- and down-regulation of many of the genes in our dataset had a clear glucose dependence in the parent V5 strain that was not present in V5.TM6*P. This important result indicates that the relief of glucose repression is already operable at much higher glucose concentrations than is widely accepted and suggests that glucose sensing might occur inside the cell.
+  Conclusions
+  Our dataset gives a remarkably complete view of the involvement of genes in the TCA cycle, glyoxylate cycle and respiratory chain in the expression of the phenotype of V5.TM6*P. Furthermore, 88 % of the transcriptional response of the induced genes in our dataset can be related to the potential activities of just three transcription factors; Hap2/3/5, Cat8 and Mig1. Overall, our data support genetic remodelling in V5.TM6*P consistent with a respiratory metabolism which is insensitive to external glucose concentrations.
+:arrays: 
+  GSM298504: 
+    condition: V4_WILDTY_22
+  GSM298494: 
+    condition: T6_MUTANT_18
+  GSM298483: 
+    condition: T3_MUTANT_15
+  GSM298505: 
+    condition: V4_WILDTY_22
+  GSM298506: 
+    condition: V5_WILDTY_23
+  GSM298484: 
+    condition: T3_MUTANT_15
+  GSM298496: 
+    condition: V1_WILDTY_19
+  GSM298485: 
+    condition: T4_MUTANT_16
+  GSM298508: 
+    condition: V5_WILDTY_23
+  GSM298497: 
+    condition: V1_WILDTY_19
+  GSM298509: 
+    condition: V6_WILDTY_24
+  GSM298487: 
+    condition: T4_MUTANT_16
+  GSM298510: 
+    condition: V6_WILDTY_24
+  GSM298477: 
+    condition: T1_MUTANT_13
+  GSM298500: 
+    condition: V2_WILDTY_20
+  GSM298489: 
+    condition: T5_MUTANT_17
+  GSM298478: 
+    condition: T2_MUTANT_14
+  GSM298501: 
+    condition: V2_WILDTY_20
+  GSM298491: 
+    condition: T5_MUTANT_17
+  GSM298480: 
+    condition: T2_MUTANT_14
+  GSM298502: 
+    condition: V3_WILDTY_21
+  GSM298492: 
+    condition: T6_MUTANT_18
+  GSM298503: 
+    condition: V3_WILDTY_21
+  GSM298426: 
+    condition: T1_MUTANT_13
+:title: Transcriptome data - Respiratory S. cerevisiae Strain Phenotype is Glucose Insensitive and vital TFs are Hap4 Cat8 Mig1
+:platform: GPL4423

data/install_scripts/GEO/series/GSE11856.yaml

@@ -0,0 +1,11 @@
+--- 
+:description: We employed CapitalBio Corporation to investigate the global transcriptional profiling of Saccharomyces cerevisiae  treated with allicin.
+:arrays: 
+  GSM299444: 
+    treatment: AllicinvsDMSO
+  GSM299445: 
+    treatment: AllicinvsDMSO
+  GSM299446: 
+    treatment: AllicinvsDMSO
+:title: Global transcriptional profiling of Saccharomyces cerevisiae treated with allicin
+:platform: GPL6010

data/install_scripts/GEO/series/GSE11878.yaml

@@ -0,0 +1,19 @@
+--- 
+:description: |-
+  Transcriptional profiling of Saccharomyces cerevisiae cells comparing the W303-1A wildtype with the W303-1A double mutant for MSN2 and MSN4 during zinc deficient conditions
+  Keywords: Genetic modification with zinc limitation
+:arrays: 
+  GSM300098: 
+    treatment: msn2-4 vs wt
+  GSM300099: 
+    treatment: msn2-4 vs wt
+  GSM300094: 
+    treatment: msn2-4 vs wt
+  GSM300095: 
+    treatment: msn2-4 vs wt
+  GSM300096: 
+    treatment: msn2-4 vs wt
+  GSM300097: 
+    treatment: msn2-4 vs wt
+:title: "Saccharomyces cerevisiae cells: W303-1A vs W303-1A delta MSN2, MSN4"
+:platform: GPL6890

data/install_scripts/GEO/series/GSE11983.yaml

@@ -0,0 +1,15 @@
+--- 
+:description: |-
+  The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status.  Zap1 acts as both a positive and negative regulator of its target genes.  We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome.  In this study, we have used complementary methods to identify additional Zap1 target genes.  With alternative growth conditions for the microarray experiments and a more sensitive motif identification algorithm, we have identified 31 new potential targets of Zap1 activation.
+  Keywords: Yeast Saccharomyces cerevisiae whole genome array
+:arrays: 
+  GSM303320: 
+    condition: Zap1TC-allele vs. vector 1uM zinc
+  GSM303319: 
+    condition: Zap1TC-allele vs. vector 1uM zinc
+  GSM303321: 
+    condition: LZM3 vs. LZM3000 3uM zinc
+  GSM303322: 
+    condition: LZM3 vs. LZM3000 3uM zinc
+:title: Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae
+:platform: GPL7018

data/install_scripts/GEO/series/GSE12004.yaml

@@ -0,0 +1,41 @@
+--- 
+:description: Oxygen lack of various severity can force many organisms to enter into recoverable hypometabolic states. To better understand how organisms cope with oxygen deprivation, our lab had previously shown that when challenged with anoxia, both the nematode Caenorhabditis elegans and embryos of the zebrafish Danio rerio enter into suspended animation, where all life processes that can be observed by light microscopy reversibly halt, pending restoration of oxygen. Here, we show that both sporulating and vegetative cells of the budding yeast Saccharomyces cerevisiae also enter into a similar state of suspended animation when made anoxic on a non-fermentable carbon source. Transcriptional profiling using cDNA microarrays shows upregulation of aerobic metabolism genes in carbon monoxide (CO)-induced anoxia, but not nitrogen (N2) gas-induced anoxia, consistent with the known oxygen-mimetic effects of CO.  Our results lead us to propose a model for oxygen-regulated gene expression in yeast where two oxygen-sensitive mechanisms operate simultaneously, such that treatment with N2 results in both mechanisms signaling a lack of oxygen, while treatment with CO results in one sensing mechanism signaling a lack of oxygen, while the other signals an abundance of oxygen.
+:arrays: 
+  GSM303509: 
+    time: 45min
+    treatment: acetate_CO
+  GSM303513: 
+    time: 45min
+    treatment: acetate_N2
+  GSM303514: 
+    time: 60min
+    treatment: acetate_CO
+  GSM303515: 
+    time: 60min
+    treatment: acetate_N2
+  GSM303504: 
+    time: 15min
+    treatment: acetate_CO
+  GSM303516: 
+    time: 120min
+    treatment: acetate_CO
+  GSM303505: 
+    time: 15min
+    treatment: acetate_N2
+  GSM303517: 
+    time: 120min
+    treatment: acetate_N2
+  GSM303506: 
+    time: 30min
+    treatment: yeast_on_acetate_CO_acetate_CO
+  GSM303518: 
+    time: 24h
+    treatment: acetate_CO
+  GSM303519: 
+    time: 24h
+    treatment: acetate_N2
+  GSM303508: 
+    time: 30min
+    treatment: acetate_N2
+:title: Transcriptional profiles of yeast on acetate exposed to pure nitrogen or carbon monoxide
+:platform: GPL1914

data/install_scripts/GEO/series/GSE12055.yaml

@@ -0,0 +1,109 @@
+--- 
+:description: |-
+  We examined the gene expression
+  changes resulting from the evolution of resistance in
+  experimental populations of the yeast Saccharomyces
+  cerevisiae subjected to two antifungal drugs, fluconazole
+  (FLC) and amphotericin B (AmB). Fluconazole resistance may involve increased efflux or changes in sterol metabolism, while AmB resistance
+  generally involves changes in sterol metabolism; for all of
+  these types of resistance, the gene expression changes are
+  extensive. The goal of these experiments was to test
+  whether failure of gene expression changes all downstream
+  of the original mutation for drug resistance would affect
+  the ability of a mutant cell to evolve and/or to support a
+  drug-resistant phenotype.
+:arrays: 
+  GSM304456: 
+    condition: Sce15vsSce2469
+  GSM97179: 
+    condition: Sce14vsSce27
+  GSM97168: 
+    condition: Sce13vsSce26
+  GSM97157: 
+    condition: Sce1113vsSce100
+  GSM97180: 
+    condition: Sce15vsSce28
+  GSM97158: 
+    condition: Sce13vsSce17
+  GSM304468: 
+    condition: Sce15vsSce2542
+  GSM304457: 
+    condition: Sce16vsSce2470
+  GSM304435: 
+    condition: Sce14vsSce2468
+  GSM304424: 
+    condition: Sce14vsSce2468
+  GSM97181: 
+    condition: Sce15vsSce28
+  GSM97159: 
+    condition: Sce13vsSce17
+  GSM304470: 
+    condition: Sce15vsSce2542
+  GSM304458: 
+    condition: Sce16vsSce2470
+  GSM97182: 
+    condition: Sce509vsSce100
+  GSM97160: 
+    condition: Sce13vsSce17
+  GSM304471: 
+    condition: Sce15vsSce2542
+  GSM304460: 
+    condition: Sce14vsSce2539
+  GSM304459: 
+    condition: Sce16vsSce2470
+  GSM97183: 
+    condition: Sce509vsSce100
+  GSM97161: 
+    condition: Sce13vsSce17
+  GSM304461: 
+    condition: Sce14vsSce2539
+  GSM97162: 
+    condition: Sce14bs Sce18
+  GSM304473: 
+    condition: Sce15vsSce14
+  GSM304462: 
+    condition: Sce14vsSce2539
+  GSM304439: 
+    condition: Sce14vsSce2468
+  GSM97163: 
+    condition: Sce14bs Sce18
+  GSM97152: 
+    condition: Sce13vsSce1060
+  GSM97175: 
+    condition: Sce13vsSce26
+  GSM97164: 
+    condition: Sce15vsSce19
+  GSM97153: 
+    condition: Sce13vsSce1060
+  GSM304475: 
+    condition: Sce16vsSce14
+  GSM304464: 
+    condition: Sce14vsSce2539
+  GSM304442: 
+    condition: Sce14vsSce2468
+  GSM97176: 
+    condition: Sce14vsSce27
+  GSM97165: 
+    condition: Sce15vsSce19
+  GSM97154: 
+    condition: Sce13vsSce1089
+  GSM304454: 
+    condition: Sce15vsSce2469
+  GSM97177: 
+    condition: Sce14vsSce27
+  GSM97166: 
+    condition: Sce13vsSce26
+  GSM97155: 
+    condition: Sce13vsSce1089
+  GSM304477: 
+    condition: Sce15vsSce16
+  GSM304455: 
+    condition: Sce15vsSce2469
+  GSM97178: 
+    condition: Sce14vsSce27
+  GSM97167: 
+    condition: Sce13vsSce26
+  GSM97156: 
+    condition: Sce1113vsSce100
+:title: Gene Expression and evolution of antifungal drug resistance
+:platform: GPL3458